[English] 日本語
Yorodumi- PDB-7u4s: Structure of Glyceraldehyde-3-Phosphate Dehydrogenase from Candid... -
+Open data
-Basic information
Entry | Database: PDB / ID: 7u4s | ||||||
---|---|---|---|---|---|---|---|
Title | Structure of Glyceraldehyde-3-Phosphate Dehydrogenase from Candida albicans | ||||||
Components | Glyceraldehyde-3-phosphate dehydrogenaseGlyceraldehyde 3-phosphate dehydrogenase | ||||||
Keywords | OXIDOREDUCTASE / Glyceraldehyde-3-Phosphate Dehydrogenase | ||||||
Function / homology | Function and homology information glyceraldehyde-3-phosphate dehydrogenase (phosphorylating) / glyceraldehyde-3-phosphate dehydrogenase (NAD+) (phosphorylating) activity / glycolytic process / cell wall organization / glucose metabolic process / NAD binding / NADP binding / extracellular region / cytoplasm Similarity search - Function | ||||||
Biological species | Candida albicans WO-1 (yeast) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.68 Å | ||||||
Authors | Miranda, R.R. / Silva, M. / Iulek, J. | ||||||
Funding support | Brazil, 1items
| ||||||
Citation | Journal: Chem. Data Coll. / Year: 2022 Title: Expression, purification, crystallization and structure of Glyceraldehyde-3-Phosphate Dehydrogenase from Candida albicans, main causative agent of candidiasis Authors: Miranda, R.R. / Silva, M. / Iulek, J. | ||||||
History |
|
-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
---|
-Downloads & links
-Download
PDBx/mmCIF format | 7u4s.cif.gz | 592.1 KB | Display | PDBx/mmCIF format |
---|---|---|---|---|
PDB format | pdb7u4s.ent.gz | 408.6 KB | Display | PDB format |
PDBx/mmJSON format | 7u4s.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/u4/7u4s ftp://data.pdbj.org/pub/pdb/validation_reports/u4/7u4s | HTTPS FTP |
---|
-Related structure data
Related structure data | 4iq8S S: Starting model for refinement |
---|---|
Similar structure data | Similarity search - Function & homologyF&H Search |
-Links
-Assembly
Deposited unit |
| ||||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|
1 |
| ||||||||||||
Unit cell |
|
-Components
#1: Protein | Mass: 35924.852 Da / Num. of mol.: 4 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Candida albicans WO-1 (yeast) / Strain: WO-1 / Gene: TDH1, GAP, TDH3, CAWG_02997 / Production host: Escherichia coli (E. coli) References: UniProt: Q92211, glyceraldehyde-3-phosphate dehydrogenase (phosphorylating) #2: Chemical | #3: Water | ChemComp-HOH / | Has ligand of interest | N | |
---|
-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION / Number of used crystals: 1 |
---|
-Sample preparation
Crystal | Density Matthews: 2.78 Å3/Da / Density % sol: 55.76 % |
---|---|
Crystal grow | Temperature: 291.15 K / Method: vapor diffusion, hanging drop Details: 20% w/v PEG6000 0.1 M citrate, pH 4.0, 1.0 M lithium chloride |
-Data collection
Diffraction | Mean temperature: 100 K / Serial crystal experiment: N |
---|---|
Diffraction source | Source: SYNCHROTRON / Site: SOLEIL / Beamline: PROXIMA 1 / Wavelength: 0.97856 Å |
Detector | Type: DECTRIS EIGER X 16M / Detector: PIXEL / Date: Sep 9, 2020 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.97856 Å / Relative weight: 1 |
Reflection | Resolution: 2.68→72.52 Å / Num. obs: 44083 / % possible obs: 100 % / Redundancy: 13 % / Biso Wilson estimate: 40.72 Å2 / CC1/2: 0.966 / Rpim(I) all: 0.183 / Net I/σ(I): 4.7 |
Reflection shell | Resolution: 2.68→2.75 Å / Redundancy: 7 % / Num. unique obs: 3258 / CC1/2: 0.4 / Rpim(I) all: 2.205 / % possible all: 100 |
-Processing
Software |
| |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: PDB entry 4IQ8 Resolution: 2.68→72.52 Å / SU ML: 0.4565 / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 32.4152 Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
| |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Solvent computation | Shrinkage radii: 1.1 Å / VDW probe radii: 1.2 Å / Solvent model: FLAT BULK SOLVENT MODEL | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 53.29 Å2 | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 2.68→72.52 Å
| |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refine LS restraints |
| |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
LS refinement shell |
| |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement TLS params. | Method: refined / Refine-ID: X-RAY DIFFRACTION
| |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement TLS group | Refine-ID: X-RAY DIFFRACTION / Auth seq-ID: 1 - 335
|